Error in creating the standard Kraken2 database
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Entering edit mode
8 months ago

Hello I'm trying to create the standard Kraken 2 database, with the following command:

kraken2-build --standard --threads 16 --db kraken-Sdb

I' getting this:

Step 1/2: Performing rsync file transfer of requested files
Rsync file transfer complete.
Step 2/2: Assigning taxonomic IDs to sequences
All files processed, cleaning up extra sequence files... done, library complete.
Masking low-complexity regions of downloaded library... done.
Step 1/2: Performing rsync file transfer of requested files
Rsync file transfer complete.
Step 2/2: Assigning taxonomic IDs to sequences
All files processed, cleaning up extra sequence files... done, library complete.
Masking low-complexity regions of downloaded library... done.
Step 1/2: Performing rsync file transfer of requested files
Rsync file transfer complete.
Step 2/2: Assigning taxonomic IDs to sequences
All files processed, cleaning up extra sequence files... done, library complete.
Masking low-complexity regions of downloaded library... done.
Downloading plasmid files from FTP...
gzip: plasmid.6.1.genomic.fna.gz: invalid compressed data--format violated

gzip: plasmid.7.1.genomic.fna.gz: invalid compressed data--format violated

gzip: plasmid.8.1.genomic.fna.gz: invalid compressed data--format violated

gzip: plasmid.9.1.genomic.fna.gz: invalid compressed data--format violated

Any thoughts how I can solve this problem?

Thank you Nathalia

kraken2 plasmid format violated • 609 views
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Entering edit mode

It seems like the data is corrupted, and it also seems like it is a custom database. So, I couldn't understand the reason of downloading files, don't you already have them?

You can try to download some of the files from ftp by yourself, not with kraken2, and try to gunzip it to see if it works. I'm pretty sure the error source is not kraken2.

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Entering edit mode

I'm having the exact same problem. I'm thinking a simple solution would be to skip the plasmid libraries. These files are definitely being downloaded wrong

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